Abstract

Background

Site-specific transcription factors (TFs) bind DNA regulatory elements to control
expression of target genes, forming the core of gene regulatory networks. Despite
decades of research, most studies focus on only a small number of TFs and the roles
of many remain unknown.

Results

We present a systematic characterization of spatiotemporal gene expression patterns
for all known or predicted Drosophila TFs throughout embryogenesis, the first such comprehensive study for any metazoan
animal. We generated RNA expression patterns for all 708 TFs by in situ hybridization, annotated the patterns using an anatomical controlled vocabulary,
and analyzed TF expression in the context of organ system development. Nearly all
TFs are expressed during embryogenesis and more than half are specifically expressed
in the central nervous system. Compared to other genes, TFs are enriched early in
the development of most organ systems, and throughout the development of the nervous
system. Of the 535 TFs with spatially restricted expression, 79% are dynamically expressed
in multiple organ systems while 21% show single-organ specificity. Of those expressed
in multiple organ systems, 77 TFs are restricted to a single organ system either early
or late in development. Expression patterns for 354 TFs are characterized for the
first time in this study.

Conclusions

We produced a reference TF dataset for the investigation of gene regulatory networks
in embryogenesis, and gained insight into the expression dynamics of the full complement
of TFs controlling the development of each organ system.